: for next, iGEMers and synthetic biologists

Overview:

  Previous participants of iGEM suggested creative ideas and developed simple and portable products based on the improvement of parts. Breaking the limitation of subjects, we, Sogang_Korea, challenged a project on integrated science & engineering that converged synthetic biology, chemistry, mechanical engineering, computer science, education, and social welfare. We propose a new course, especially robotics, to worldwide iGEMers with the success of ‘SynBioBot’.

  The goals were automation and education of synthetic biological experiments, such as cell culturing and transduction of lentiviral. To acheive goals with robots, we must develop an algorithm of overall robot movement, and a method of electronic signal transmitting and receiving(the wiring work). Additionally, we should design supporting parts, based on material dynamics and useful designs, for the robotic arm to handle experimental apparatus easily. All processes of development were organically connected to each other. To complete gesture coding, we should have created all supporting parts to apply gripper on experiment tools. To complete creating them, we should have prepared materials for the environment setting. We developed the SynBioBot-optimized design helix and utilized a cooperation tool, Notion, to effectively control time. With all of our efforts, we successfully connected a variety of studies into one.

  The effort might seem to be a small step for team Sogang_Korea, but it is a big leap for future iGEM.


Fig 1. Motion Algorithm Scheme

  Robots as a tool for experimentation are totally effective. It would not get tired and makes little mistakes in motions, unlike human beings. Yet, we should go through arduous progress to implement a robot, that does what we want.

  The foremost step is to check every motion and decision process of humans and convert them to the robot’s motions. Accomplishing the first step, we made an algorithm diagram- the scheme - to arrange gestures. You may check what we have done in Fig 1.

  If we say the overall project is a large vessel, the scheme is a helmsman. It helps us not to get lost and to write efficient codes. Schemes are seriously difficult to work on without any references or examples since there are too many decisions done by a human while conducting every single part of a motion. However, scheme examples support newbies to robotics, it is easy to compare and follow the process and change one by one with their preferences and demand. In this regard, products of the project ‘SynBioBot’ let future iGEMers not hesitate, but to do an assertive challenge on robots.


Fig 2. Incubator Opening Motion Mode

  Additionally, we possess every process, motion, and vision control method of cell culturing and transduction into Python code. If you are the one who needs them and checked this comment, please get in touch with us via E-mail or Instagram DM so that we can have the pleasure to provide what we have got.


Wiring Work


Fig 3. Control box Circuit

  The two-fingered gripper we bought from OnRobot, Inc. has compatibility and interoperability with a variety of robot arms. For instance, they provide collaboration cases of huge robot companies such as Universal Robots, Doosan, Fanuc, etc. However, they have not possessed any data with the robot arm ‘ZERO’ from Global Zeus. The data we received instead was Doosan, but it did not work. To overcome the problem, we studied the control box circuit and cooperated with OnRobot, Inc. At last, we successfully completed the wiring work for sending & receiving data between the robot arm and the gripper.

  Actually, a lot of wiring works, even if they are logically perfect, often do not operate well. Therefore, we wish iGERMers feel free to apply our wiring work to lessen the burdensome of trying robotics with the robot arm ‘ZERO’.

  The details of wiring work can be checked on HARDWARE(Wiring Work).


3D Modeling


Fig 4. Pipette with the human hand / Fig5. Pipette with the two-fingered gripper and the pipette case

  We upgraded several experimental tools that are always used in experiments to cooperate with a robot arm with just two fingers. 3D CAD modeling and printing were significant.

  Almost every biology experiments require pipetting. Pipettes are designed for human hands as you can check in Fig 4. We discussed and shared ideas for a long time to apply a robot arm with two-finger. We, finally, developed a supporting part to handle the pipette with two finger gripper, that can be easily manufactured by a 3D printer and assembled. The item called ‘the pipette case’ is light and strong, perfect for the experiment. You may check the details on HARDWARE(Pipette Case).

  Recently, we obtained patents for a pipette case, but we wish future iGEMers to use this item for free except for commercial purposes.


Developing design helix & Utilizing cooperation tool


  As we mentioned in the above overview, all of our projects were interconnected. From environment setting to python coding, we should have done those almost simultaneously. While developing the project on robotics, we were also required to solve problems on communication for sponsorship, patent work, and education for high school students. We recognized that the time and the process for each work should be organized well and the sharing of files and documents should be done in real-time.

  First and foremost, we modeled the overall project diagram by optimizing the design helix for manufacturing. Fig 6 is an optimized design helix for the ‘SynBioBot’ project. This demonstrates below statements;


  1.   The process can begin at any stage or any place. and as a function of the time spent and the effort spent, we move to the next stage.
  2.   Conversely, just because the environment is set, robot movements are coded, and experiments & problems are progressed or solved, we should not regard the process as being completed.
  3.   One must identify new information from the present situation and develop the robotics coding-environment setting-experiment & solving problem strategies for the next generation of improvement.
  4.   We need to deal with both micro- and macro- issues, and develop models for dynamic interaction amongst the elements of the SynBioBot-optimized design helix.

Fig 6. SynBioBot-optimized design helix

  Next, we used a cooperation tool called Notion.

  Unlike other cooperation tools, Notion provides both scheduling calendars and a workspace for composing and sharing documents. Also, we can customize the workspace according to the importance and the access degree of documents. We maximized the advantages of Notion and completed nearly 80 % of the robotic processes in 2.5 months. We, the team Sogang_Korea, wish our experiences of us could help future iGEMers diminish the waste of time and concentrate on the research of synthetic biology.

Fig 7. Scheduling and Sharing by Notion

Reference:

1. Nam P. SUH (1990). The Principles of Design (Oxford Series on Advanced Manufacturing, 6). New York, Oxford University Press, Inc.